separate out into a function so we can send any alignment and "fix" it.
separate out into a function so we can send any alignment and "fix" it.

PeteHaitch/bwa-parclip,dariober/bwa-meth,brentp/bwa-meth,PeteHaitch/bwa-parclip,brentp/bwa-meth,dariober/bwa-meth,dariober/bwa-meth,brentp/bwa-meth,PeteHaitch/bwa-parclip